Full text loading...
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
1.C. Chipot and D. A. Pearlman, Mol. Simul. 28, 1 (2002), and references therein.
2.D. A. Pearlman and P. R. Connelly, J. Mol. Biol. 248, 696 (1995).
3.D. A. Pearlman and P. A. Kollman, J. Chem. Phys. 91, 7831 (1989).
4.C. Chipot, P. A. Kollman, and D. A. Pearlman, J. Comput. Chem. 17, 1112 (1996).
5.H. J. C. Berendsen, in Proteins: Structure, Dynamics, and Design, edited by V. Renugopalakrishnan, P. R. Carey, I. C. P. Smith, S. G. Huang, and A. C. Storer (ESCOM, Leiden, 1991), pp. 384–392.
6.W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Mertz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
7.J. A. D. MacKerell, D. Bashford, M. Bellot et al., J. Phys. Chem. B 102, 3586 (1998).
8.W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide (Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland, 1996).
9.W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 11225 (1996).
10.D. J. Price and C. L. Brooks, J. Comput. Chem. 23, 1045 (2002).
11.M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002).
12.T. Hansson, C. Oostenbrink, and W. F. Van Gunsteren, Curr. Opin. Struct. Biol. 12, 190 (2002).
13.B. Chen and J. I. Siepmann, J. Phys. Chem. B 103, 5370 (1999).
14.B. Chen, J. J. Potoff, and J. I. Siepmann, J. Phys. Chem. B 105, 3093 (2001).
15.C. D. Wick, M. G. Martin, and J. I. Siepmann, J. Phys. Chem. B 104, 8008 (2000).
16.S. K. Nath, F. A. Escobedo, and J. J. de Pablo, J. Chem. Phys. 108, 9905 (1998).
17.J. R. Errington and A. Z. Panagiotopoulos, J. Phys. Chem. B 103, 6314 (1999).
18.R. Wolfenden, L. Andersson, P. M. Cullis, and C. C. B. Southgate, Biochemistry 20, 849 (1981).
19.A. Ben-Naim and Y. Marcus, J. Chem. Phys. 81, 2016 (1984).
20.S. Cabani, P. Gianni, V. Mollica, and L. Lepori, J. Solution Chem. 10, 563 (1981).
21.J. Hine and P. K. Mookerjee, J. Org. Chem. 40, 292 (1975).
22.M. H. Abraham, G. S. Whiting, R. Fuchs, and E. J. Chambers, J. Chem. Soc., Perkin Trans. 2 2, 291 (1990).
23.V. N. Viswanadhan, A. K. Ghose, U. C. Singh, and J. J. Wendoloski, J. Chem. Inf. Comput. Sci. 39, 405 (1999).
24.In this paper, the force fields are listed alphabetically.
25.S. E. DeBolt and P. A. Kollman, J. Am. Chem. Soc. 117, 5316 (1995).
26.T. Fox and P. A. Kollman, J. Phys. Chem. B 102, 8070 (1998).
27.I. G. Tironi and W. F. Van Gunsteren, Mol. Phys. 83, 381 (1994).
28.J. E. Eksterowicz, J. L. Miller, and P. A. Kollman, J. Phys. Chem. B 101, 10971 (1997).
29.Additionally, the time scales important for equilibration and sampling can be longer than for water. For example, our initial experiments with blocked amino acids in a 1-octanol/water mixture suggested correlation times for some degrees of freedom of at least 100s of picoseconds.
30.C. Chothia, J. Mol. Biol. 105, 1 (1976).
31.A. Radzicka and R. Wolfenden, Biochemistry 27, 1664 (1988).
32.J. S. Bader and D. Chandler, J. Phys. Chem. 96, 6424 (1992).
33.H. A. Carlson, T. B. Nguyen, M. Orozco, and W. L. Jorgensen, J. Comput. Chem. 14, 1240 (1993).
34.A. Villa and A. E. Mark, J. Comput. Chem. 23, 548 (2002).
35.G. Kaminski, E. M. Duffy, T. Matsui, and W. L. Jorgensen, J. Phys. Chem. 98, 13077 (1994).
36.W. L. Jorgensen and T. B. Nguyen, J. Comput. Chem. 14, 195 (1993).
37.V. Helms and R. C. Wade, J. Am. Chem. Soc. 120, 2710 (1998).
38.B. Chen and J. I. Siepmann, J. Am. Chem. Soc. 122, 6464 (2000).
39.Produced and distributed by the Professor Jay Ponder’s research group at Washington University. Documentation and programs for TINKER are available at http://dasher.wustl.edu/tinker/.
40.M. Shirts and V. S. Pande, Science 290, 1903 (2000).
41.90 000 is the number of processors running Folding@Home worldwide at the time the paper was written. At the time the simulations were run, the number was closer to 30 000.
42.C. D. Snow, N. Nguyen, V. S. Pande, and M. Gruebele, Nature (London) 420, 102 (2002).
43.B. Zagrovic, E. J. Sorin, and V. S. Pande, J. Mol. Biol. 313, 151 (2001).
44.V. S. Pande, I. Baker, J. Chapman, S. P. Elmer, S. Khaliq, S. M. Larson, Y. M. Rhee, M. R. Shirts, C. D. Snow, E. J. Sorin, and B. Zagrovic, Biopolymers 68, 91 (2003).
45.B. Zagrovic, C. D. Snow, S. Khaliq, M. R. Shirts, and V. S. Pande, J. Mol. Biol. 323, 153 (2002).
46.S. M. Larson, C. D. Snow, M. R. Shirts, and V. S. Pande, in Computational Genomics, edited by R. P. Grant (Horizon Scientific, Wymondham, Norfolk, U.K., 2002) (in press).
47.S. M. Larson, J. L. England, J. R. Dejarlais, and V. S. Pande, Protein Sci. 11, 2804 (2002).
48.H. C. Andersen, J. Chem. Phys. 72, 2384 (1980).
49.T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, and W. F. van Gunsteren, Chem. Phys. Lett. 222, 529 (1994).
50.P. A. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot, and A. Pohorille, in Computer Simulation of Biomolecular Systems, edited by A. Wilkinson, P. Weiner, and W. F. van Gunsteren (Elsevier, Amsterdam, The Netherlands, 1997), Vol. 3, pp. 83–96.
51.G. A. Kaminski, R. A. Friesner, J. Rives, and W. L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001).
52.H. Resat and J. A. McCammon, J. Chem. Phys. 108, 9617 (1998).
53.T. P. Straatsma and H. J. C. Berendsen, J. Chem. Phys. 89, 5876 (1988).
54.See EPAPS Document No. for parameter files and a brief description. A direct link to this document may be found in the online article’s HTML reference section. The document may also be reached via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html) or from ftp.aip.org in the directory /epaps/. See the EPAPS homepage for more information.[Supplementary Material]
55.W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
56.M. L. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000).
57.W. C. Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson, J. Chem. Phys. 76, 637 (1982).
58.H. C. Andersen, J. Comput. Phys. 52, 24 (1983).
59.J. P. Ryckaert and G. Ciccotti, Mol. Phys. 58, 1125 (1986).
60.J. P. Ryckaert and G. Ciccotti, J. Chem. Phys. 78, 7368 (1983).
61.G. Ciccotti and J. P. Ryckaert, Comput. Phys. Rep. 4, 345 (1986).
62.M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
63.To reduce the effect of the noise that occurs when the correlation function approaches 0, the tail of the function was replaced by a linear fit (for the purposes of integration) between the first time the normalized correlation function reaches 0.1 and the first time it reaches 0.0 by connecting these time points. Inspection indicated that a linear approximation is more accurate than an exponential fit. This process is simplistic (and fails if the correlation function is too far from monotonically decreasing in the tail), but is of sufficient accuracy here, since we ultimately require only one significant digit in the determination of uncertainty.
64.P. J. Steinbach and B. R. Brooks, J. Comput. Chem. 15, 667 (1994).
65.In some simulations, the electrostatic potential is shifted before the switch is applied in order to minimize forces arising from sharply tapered potentials (Ref. 64). However, since all groups are neutral in these simulations, a shift actually has no net effect on intergroup interactions.
66.CRC Handbook of Chemistry and Physics, edited by D. R. Lide (CRC, Boston, 2001).
67.W. L. Jorgensen and C. Jenson, J. Comput. Chem. 19, 1179 (1998).
68.An important but rarely commented upon artifact of periodic boundary conditions in that there is a system size dependence for any observable that has nonisotropic components (Refs. 103104105). The density of water depends on the nonisotropic dipole–dipole interaction between water molecules, especially in conjunction with finite-range treatments of electrostatic interactions. A recent study of TIP5P water (Ref. 75), as well as our unpublished results have found this size-dependence of density with finite-ranged Coulombic potentials, but more work is necessary to understand this phenomenon.
69.T. P. Straatsma and J. A. McCammon, J. Chem. Phys. 95, 1175 (1991).
70.A. Dejaegere and M. Karplus, J. Phys. Chem. 100, 11148 (1996).
71.J. W. Pitera and W. F. Van Gunsteren, Mol. Simul. 28, 45 (2002).
72.A. E. Mark and W. F. Van Gunsteren, J. Mol. Biol. 240, 167 (1994).
73.J. T. Wescott, L. R. Fisher, and S. Hanna, J. Chem. Phys. 116, 2361 (2002).
74.See Ref. 54.
75.M. Lisal, J. Kolafa, and I. Nezbeda, J. Chem. Phys. 117, 8892 (2002).
76.P. Mark and L. Nilsson, J. Comput. Chem. 23, 1211 (2002).
77.A. R. Leach, Molecular Modelling: Principles and Applications (Addison–Wesley Longman Limited, Harlow, Essex, England, 1996).
78.H. Resat and M. Mezei, J. Chem. Phys. 99, 6052 (1993).
79.P. E. Smith and W. F. Van Gunsteren, J. Chem. Phys. 100, 577 (1994).
80.C. Simmerling, T. Fox, and P. A. Kollman, J. Am. Chem. Soc. 120, 5771 (1998).
81.C. D. Wick and J. I. Siepmann, Macromolecules 33, 7207 (2000).
82.Z. Chen and F. A. Escobedo, J. Chem. Phys. 113, 11382 (2000).
83.N. Rathore, T. A. Knotts, and J. J. de Pablo, J. Chem. Phys. 118, 4285 (2003).
84.V. G. Mavrantzas, T. D. Boone, E. Zervopoulou, and D. N. Theodorou, Macromolecules 32, 5072 (1999).
85.J. P. Ulmschneider and W. L. Jorgensen, J. Chem. Phys. 118, 4261 (2003).
86.D. Yin and J. Alexander D. Mackerell, J. Comput. Chem. 19, 334 (1998).
87.OPLS-AA and AMBER used some free energy simulations to gauge the general applicability of the force field for free energy calculations, but force fields were not explicitly tuned to give correct free energies—nor could they, with the precision available at the time.
88.Some recasting of the experimental data is necessary in order to convert the experimental results to the form used in this paper. In Abraham et al. (Ref. 22), and in Hine and Mookerjee (Ref. 21) the desired hydration free energy can be obtained by multiplying the Oswalt coefficient by With the data from Plyasunov and Shock (Ref. 89) we can convert from to a hydration free energy by subtracting which can be approximated by neglecting the volume in liquid state and assuming ideality the gas (Ref. 19) with an error of less than 0.01 kcal/mol.
89.A. V. Plyasunov and E. L. Shock, Geochim. Cosmochim. Acta 64, 439 (2000).
90.W. L. Jorgensen, J. D. Madura, and C. J. Swenson, J. Am. Chem. Soc. 106, 6638 (1984).
91.C. L. Lin and R. H. Wood, J. Phys. Chem. 100, 16399 (1996).
92.Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 113, 6042 (2000).
93.A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers 60, 96 (2001).
94.G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
95.C. Bartels, M. Schaefer, and M. Karplus, J. Chem. Phys. 111, 8048 (1999).
96.M. D. Beachy, D. Chasman, R. B. Murphy, T. A. Halgren, and R. A. Friesner, J. Am. Chem. Soc. 119, 5908 (1997).
97.T. A. Halgren, J. Comput. Chem. 20, 730 (1999).
98.P. M. King, Mol. Phys. 94, 717 (1998).
99.D. A. McQuarrie, Statistical Mechanics (Harper and Row, New York, 1976).
100. is referred to as in the work of Ben-Naim and Marcus (Ref. 19). They refer to this as the coupling work, or the Gibbs free energy of interaction of with the rest of the solution.
101.See discussions in Refs. 106 and 107. In general, all observable thermodynamic quantities are expressed as logarithms of ratios of partition functions, so volume scale factors cancel and the particular choice has no consequence. A particularly useful value of is since this choice gives the purely extensive expression for the Gibbs free energy of an ideal gas in Eq. (15). However, other choices give identical results for chemical potentials and solvation free energies.
102.The work described in Wescott et al. (Ref. 73) employed a different coupling scheme, whereby the contribution to the internal pressure from the “internal energy” of the special molecule of type was also coupled. Using the terminology of the current study, their coupling scheme results in a mean volume at of whereas in our coupling scheme the mean volume at is We note first that the contribution to the internal pressure from the relative kinetic energy and the intramolecular contributions to the virial from the special molecule have a time average of 0 at all values of λ, and thus need not be considered. Second, we also couple the contributions to the internal pressure from the intermolecular interactions between the special molecule and the rest of the material simply by virtue of the fact that those energy and force components and consequently also their contribution to the virial are coupled. The difference between their treatment and ours is in the handling of the contribution to the internal pressure from the center-of-mass kinetic energy of the special molecule. However, since the effect of coupling this contribution corresponds to the second step in our four-step process, its contribution to the free energy of solvation will be zero. Thus, the contribution to the internal pressure from the molecular internal energy of the coupled molecule does not actually need to be included.
103.L. R. Pratt and S. W. Haan, J. Chem. Phys. 74, 1864 (1981).
104.L. R. Pratt and S. W. Haan, J. Chem. Phys. 74, 1873 (1981).
105.M. W. Evans, Comput. Phys. Commun. 59, 495 (1990).
106.T. L. Hill, Statistical Mechanics: Principles and Selected Applications (McGraw–Hill, New York, 1956).
107.T. L. Hill, An Introduction to Statistical Thermodynamics (Addison–Wesley, Reading, Massachusetts, 1960).
Article metrics loading...